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ccs combines multiple subreads of the same SMRTbell molecule using a statistical model to produce one highly accurate consensus sequence, also called a HiFi read, along with base quality values. This tool powers the Circular Consensus Sequencing workflow in SMRT Link.

A New Paradigm in Sequencing with HiFi Reads

Advanced scientific discoveries require sequencing data that is both accurate and complete. Single Molecule, Real-Time (SMRT) Sequencing technology has evolved to a different type of long read, known as highly accurate long reads, or HiFi reads. PacBio is the only sequencing technology to offer HiFi reads that provide accuracy of >99.9%, on par with short reads and Sanger sequencing. With HiFi reads you no longer have to compromise long read lengths for high accuracy sequencing to address your toughest biological questions.


The latest ccs can be installed via the bioconda package pbccs.

Please refer to our official pbbioconda page for information on Installation, Support, License, Copyright, and Disclaimer.

Latest Version

Version 6.0.0: Full changelog here

What’s new!

ccs is now running on the Sequel IIe instrument, transferring HiFi reads directly off the instrument.
Read how ccs works on Sequel IIe!

Schematic Workflow


Input: Subreads from a single movie in PacBio BAM format (.subreads.bam).

Output: Consensus reads in a format inferred from the file extension: unaligned BAM (.bam); bgzipped FASTQ (.fastq.gz); or SMRT Link XML (.consensusreadset.xml) which also generates a corresponding unaligned BAM file.

Run on a full movie:

ccs movie.subreads.bam movie.ccs.bam

Parallelize by using --chunk. See how-to chunk.

Feel free to make ccs slightly faster via environment variables.